Cios installed in slot:255 and 253. Is that not ok? Help!

I was following a guide, I got the homebrew channel installed. I then followed these steps:

'Time to install the cIOSsYou are now on the main configuration screen. A lot of options will be available here.
Your cursor will be on the cIOS D2X Version. Use the D-Pad to change it to the newest version (all the way to the right).
Move down, and change the IOS Base to 56
Move down again, and change the IOS slot to your preferred slot. Most people use slot 249.(then install it!)
Next, you want to configure the second cIOS. This time, use base 57, and choose a different slot (250 in this tutorial)'

Only when I tried to install to 249 and 250, it gave me warnings that something would over-write (unfortunately I don't remember the exact message) in that slot. It was a UK pre-owned Wii sys update: 4.3E but it wasn't already hacked (there was no homebrew channel before I got it). So anyhow I used slot 255 (for 1st),then 253 (for 2nd).

1) Problem: I read with some loaders you need to have the cios installed in certain slots (like 249 and 250). Will this cause me any problems? Should I go back and re-install it to 249 and 250 and ignore the warning messages it gave me?

2) I tried to put the wii game file on my 16GB sandisk cruzer blade FAT32 usb flash device, it said the file was too big. I know FAT can only accept files 4GB or smaller, but if I convert the 8GB iso to WBFS, roughly how big will the new wbfs be? What I'm trying to ask is, will there be some wii games that are bigger than 4GB even when converted to wbfs? In which case I should just format to NTFS. Thanks

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Having extra cIOSs won't hurt, other than taking up some of the NAND memory space. As long as everything else looks sane (and it should if you follow the guide linked above), then everything should still work for you.

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I used 'how to hack your wii for homebrew in 5 mins' on lifehacker(it used a letterbomb exploit). I installed hackmii and boot2. (For the whole process I used an UNFORMATTED Lexar 16gb SDHC card which I'd had for a while but came out the box FAT32 and the wii recognised it: no problems that I know of!)

1) what is a NAND backup and why do I need it?

2) If I install prii loader, will my wii be region-free?

3) what is a 'newer TR remote' (what does TR stand for) my wii remote didn't work with bootmii (boot2) Also how do I stop bootmii from loading at startup instead of the normal menu?

4) I've read the FAT32 and NTFS guides, But I still am unsure: if I convert the 8GB iso to WBFS, roughly how big will the new wbfs be? Will there be some wii games that are bigger than 4GB even when converted to wbfs? In which case I should just format to NTFS. I'm asking since the guide recommends FAT32. What do you do if the file is bigger than 4gB?

5) When I installed USB loader GX I went into it (without any game files) and it gave me a message: "USB device not found, Switching to channel list mode" I only had my SDHC card in the wii but could this be showing that I need to format it even though it is FAT32 already? Can anyone explain this (I was thinking of converting my game file to wbfs and putting it on the sdhc card!)

6) I'm going to follow the guide you linked to, but do you think it would be ok to jump to 'softmods with homebrew channel installed'? Also I thought I would go ahead and try the NTFS or FAT32 guide before re-hacking. Then I'll re-hack regardless but just wanted to check. Hope you can answer my questions, thanks!

Thanks for the quick reply. Some of the stuff is still not clear, it's a little more confusing when reading through since I'm trying to remember which stuff I did differently. I couldn't find answer to 4) and 5) or at least in a way that I understood. Could someone help me out, I'm still confused!

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If you don't have a USB drive attached, then "USB not found" is expected. It won't magically look for SD cards unless you tell it to. Which isn't really recommended due to the speed difference between SD and USB devices.

ISOs that are 9gigs in size will be more than 4.5gigs when converted to wbfs (otherwise the dual-layered disk wouldn't be required). If you properly install a game to a FAT32-formatted hard drive, the wbfs format will split itself along the 4gig file size so the game will fit. All USB Loaders will know how to handle this. See the FAT32 guide for several examples of how to "properly install a game".

Though, if you have any issues with anything and you've not remodded your system using Softmod Any Wii guide, then you will be asked to do so before anyone helps you (and in most of the cases, the remod using our guide will fix the problem). If you want support of your system from that other guide you followed, you should seek their assistance. If you want our help, you have to do our little dance. (Apple won't support Dell computers, for example. We won't support someone else's guide).

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I started re modding using the linked guide. I jumped to 'softmods with HBC installed', downloaded 'wiimod 58-61 hackmii' then the modpack.zip and when I merged some folders (when transferring to my sd card) it then asked me about 'boot.dol' shall I copy and replace or copy and keep both files? (it would make boot(2).dol)?

You realize you have to format and copy stuff to the SD card like three times, right? It sounds like you're ignoring the instructions of the guide. This would not be happening if you correctly following it.

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Rats I wasn't thinking, I forgot when you format then it deletes! I thought I would download/transfer the filesI needed in one go. Ok I'll delete everything and restart step by step, thanks. But the 1st time round I used my sd card without reformatting at all. Can I just delete stuff instead, or is there another reason for re-formatting?